Data is available on Synapse.
Summary
This includes code and plots for the final version of the paper. Exploratory analysis and intermediate processing steps are too extensive to be included here
## Warning: replacing previous import 'igraph::union' by 'GSEABase::union'
## when loading 'HTSanalyzeR'
Sendai Expression

Biotype of expressed genes
|
Biotype
|
Count
|
|
protein_coding
|
11681
|
|
processed_transcript
|
1691
|
|
antisense
|
1488
|
|
lincRNA
|
879
|
|
processed_pseudogene
|
822
|
|
nonsense_mediated_decay
|
708
|
|
retained_intron
|
671
|
|
sense_intronic
|
197
|
|
unprocessed_pseudogene
|
163
|
|
sense_overlapping
|
93
|
|
miRNA
|
66
|
|
misc_RNA
|
58
|
|
snoRNA
|
56
|
|
transcribed_unprocessed_pseudogene
|
47
|
|
pseudogene
|
37
|
|
transcribed_processed_pseudogene
|
28
|
|
snRNA
|
27
|
|
unitary_pseudogene
|
16
|
|
3prime_overlapping_ncrna
|
12
|
|
rRNA
|
8
|
|
Mt_tRNA
|
4
|
|
polymorphic_pseudogene
|
4
|
|
non_stop_decay
|
3
|
|
IG_V_pseudogene
|
1
|
|
TR_C_gene
|
1
|
Check sex on 94 samples

genes_on_chrY
USP9Y
UTY
NLGN4Y
ZFY
RPS4Y1
TXLNG2P
Detect sample contamination with VerifyBamID
The labeling of Donor 499 was corrected manually 
Excluded due to sample mislabeling, contamination or issues with expression on the sex chromosomes
|
Sample.Name
|
|
1275-B-3F
|
|
1275-B-3N
|
|
1275-C-1F
|
|
1275-C-1N
|
|
2476-1-4F
|
|
2476-1-4N
|
|
2484-2aF
|
|
2484-2aN
|
|
3113-3-21F
|
|
3113-3-21N
|
|
3121-2-1F
|
|
3121-2-1N
|
|
3121-2-MSSM2F
|
|
3121-2-MSSM2N
|
|
3130-2-1F
|
|
3130-2-1N
|
|
676-1-2N
|
Samples included in analysis
|
|
6_wk_FB_neuron
|
NPC
|
|
CT
|
20
|
20
|
|
SZ
|
19
|
18
|
QC metrics

Check sex on cleaned dataset

Differential gene expression based on Sendai virus exression
[1] “DE genes at FDR < 5%: 2768”
Yaminaka factors
POU5F1 is not expressed at a sufficient level
| ENSG00000136997 |
0.3021708 |
3.1929949 |
2.1221004 |
0.0371472 |
0.0849684 |
MYC |
| ENSG00000181449 |
-0.0561620 |
8.7614381 |
-1.0330145 |
0.3049324 |
0.2815826 |
SOX2 |
| ENSG00000136826 |
-0.1388002 |
0.0752657 |
-0.8533798 |
0.3961789 |
0.3249660 |
KLF4 |


Compare Neurons and NPC


Enrichments for genes up in Neurons
|
Gene Set
|
Gene Set Size
|
Expected Hits
|
Observed Hits
|
OR
|
Pvalue
|
|
tissue_exp_brain
|
495.00
|
65.97
|
241
|
3.65
|
9.20E-84
|
|
c2.BENPORATH_ES_WITH_H3K27ME3
|
730.00
|
97.29
|
283
|
2.91
|
2.29E-70
|
|
c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3
|
347.00
|
46.25
|
162
|
3.50
|
7.81E-53
|
|
c2.BENPORATH_SUZ12_TARGETS
|
664.00
|
88.50
|
240
|
2.71
|
9.40E-53
|
|
c2.BENPORATH_EED_TARGETS
|
705.00
|
93.96
|
240
|
2.55
|
2.13E-47
|
|
c2.BENPORATH_PRC2_TARGETS
|
391.00
|
52.11
|
163
|
3.13
|
5.01E-45
|
|
c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP
|
1225.00
|
163.27
|
340
|
2.08
|
1.26E-44
|
|
c2.MIKKELSEN_MCV6_HCP_WITH_H3K27ME3
|
285.00
|
37.98
|
129
|
3.40
|
2.42E-40
|
|
c2.MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3
|
215.00
|
28.65
|
108
|
3.77
|
3.83E-39
|
|
c5.GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMBRANE
|
998.00
|
133.01
|
282
|
2.12
|
3.13E-38
|
|
c5.GO_CELL_CELL_SIGNALING
|
502.00
|
66.91
|
173
|
2.59
|
7.35E-35
|
|
c5.GO_NEURON_PART
|
1088.00
|
145.01
|
282
|
1.94
|
5.04E-31
|
|
c2.MIKKELSEN_NPC_HCP_WITH_H3K27ME3
|
192.00
|
25.59
|
90
|
3.52
|
7.31E-30
|
|
c2.NABA_MATRISOME
|
555.00
|
73.97
|
174
|
2.35
|
2.58E-29
|
|
c5.GO_SYNAPSE
|
677.00
|
90.23
|
198
|
2.19
|
7.62E-29
|
|
c5.GO_SYNAPTIC_SIGNALING
|
331.00
|
44.11
|
123
|
2.79
|
1.94E-28
|
|
c2.ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY
|
873.00
|
116.35
|
235
|
2.02
|
2.55E-28
|
|
c2.SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN
|
223.00
|
29.72
|
96
|
3.23
|
3.72E-28
|
|
tissue_exp_testis
|
452.00
|
60.24
|
149
|
2.47
|
9.65E-28
|
|
c5.GO_METAL_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY
|
298.00
|
39.72
|
112
|
2.82
|
1.80E-26
|

Enrichments for genes up in NPCs
|
Gene Set
|
Gene Set Size
|
Expected Hits
|
Observed Hits
|
OR
|
Pvalue
|
|
c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP
|
547
|
33.21
|
260
|
7.83
|
4.96E-176
|
|
c2.DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP
|
304
|
18.46
|
190
|
10.29
|
1.04E-156
|
|
c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED
|
690
|
41.89
|
247
|
5.90
|
7.73E-131
|
|
c2.KOBAYASHI_EGFR_SIGNALING_24HR_DN
|
236
|
14.33
|
153
|
10.68
|
6.86E-129
|
|
c4.MODULE_54
|
241
|
14.63
|
150
|
10.25
|
2.58E-122
|
|
c2.ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER
|
137
|
8.32
|
111
|
13.34
|
2.69E-111
|
|
c7.GSE15750_DAY6_VS_DAY10_TRAF6KO_EFF_CD8_TCELL_UP
|
186
|
11.29
|
122
|
10.80
|
3.20E-103
|
|
c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP
|
1176
|
71.40
|
282
|
3.95
|
6.11E-101
|
|
c2.SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6
|
416
|
25.26
|
170
|
6.73
|
6.49E-99
|
|
c7.GSE15750_DAY6_VS_DAY10_EFF_CD8_TCELL_UP
|
189
|
11.48
|
119
|
10.37
|
1.86E-97
|
|
c5.GO_CHROMOSOME
|
778
|
47.24
|
226
|
4.78
|
2.87E-97
|
|
c2.CHANG_CYCLING_GENES
|
145
|
8.80
|
103
|
11.70
|
1.19E-92
|
|
c5.GO_CHROMOSOME_ORGANIZATION
|
875
|
53.13
|
233
|
4.39
|
8.60E-92
|
|
c2.SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP
|
147
|
8.93
|
102
|
11.43
|
4.80E-90
|
|
c2.ZHANG_TLX_TARGETS_60HR_DN
|
263
|
15.97
|
131
|
8.20
|
3.32E-89
|
|
c2.REACTOME_CELL_CYCLE
|
384
|
23.31
|
155
|
6.65
|
6.43E-89
|
|
h.HALLMARK_E2F_TARGETS
|
199
|
12.08
|
115
|
9.52
|
5.45E-88
|
|
c2.PUJANA_BRCA2_PCC_NETWORK
|
388
|
23.56
|
153
|
6.49
|
5.80E-86
|
|
c7.GSE13547_CTRL_VS_ANTI_IGM_STIM_BCELL_12H_UP
|
171
|
10.38
|
105
|
10.11
|
3.42E-84
|
|
c2.WHITEFORD_PEDIATRIC_CANCER_MARKERS
|
110
|
6.68
|
86
|
12.88
|
1.49E-83
|

Overlap between NPC and neuron
## [1] "cutoff: log2 RPKM > 0"

## [1] "cutoff: log2 RPKM > 1"

## [1] "cutoff: log2 RPKM > 2"

## [1] "cutoff: log2 RPKM > 3"

## [1] "cutoff: log2 RPKM > 4"

## [1] "cutoff: log2 RPKM > 5"

## [1] "cutoff: log2 RPKM > 6"


Cibersort results
Histogram of cell type composition: all samples

There is no case-control difference in cell type scores


Cell composition in Neurons and NPC

Differential expression based on cell fraction
Enrichment test for gene positively correlated with cell fraction
6_wk_FB_neuron-Astrocytes
| CMC-modules_peru |
114 |
68 |
108 |
1.6 |
3.3e-18 |
| CMC-modules_lightgreen |
199 |
118 |
173 |
1.5 |
8.7e-18 |
| c4.MODULE_1 |
318 |
189 |
253 |
1.3 |
7.0e-15 |
| c2.LEE_BMP2_TARGETS_UP |
598 |
355 |
443 |
1.2 |
9.2e-15 |
| c4.MODULE_47 |
196 |
116 |
162 |
1.4 |
1.4e-12 |
| c5.GO_EXTRACELLULAR_STRUCTURE_ORGANIZATI |
220 |
130 |
179 |
1.4 |
1.6e-12 |
| c2.MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H |
826 |
490 |
584 |
1.2 |
1.9e-12 |
| h.HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSI |
177 |
105 |
148 |
1.4 |
2.1e-12 |
| c4.MODULE_2 |
328 |
195 |
252 |
1.3 |
1.0e-11 |
| c2.BOQUEST_STEM_CELL_UP |
207 |
123 |
168 |
1.4 |
1.1e-11 |
6_wk_FB_neuron-Neuron
| tissue_exp_brain |
495 |
339 |
438 |
1.3 |
3.1e-26 |
| CMC-modules_red |
689 |
472 |
566 |
1.2 |
9.5e-17 |
| CMC-modules_blue |
1154 |
791 |
902 |
1.1 |
2.7e-14 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
238 |
294 |
1.2 |
2.0e-12 |
| c5.GO_SYNAPTIC_SIGNALING |
331 |
227 |
278 |
1.2 |
6.5e-11 |
| c5.GO_CELL_CELL_SIGNALING |
502 |
344 |
403 |
1.2 |
1.3e-09 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
113 |
146 |
1.3 |
1.4e-09 |
| abnormal_synaptic_transmission |
386 |
264 |
315 |
1.2 |
3.1e-09 |
| secondary_FMRP-targets |
770 |
528 |
599 |
1.1 |
3.1e-09 |
| c5.GO_SYNAPSE |
677 |
464 |
530 |
1.1 |
5.0e-09 |
6_wk_FB_neuron-Oligodendrocyte_Precursor_Cell
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
780 |
920 |
1.2 |
3.9e-19 |
| CMC-modules_peru |
114 |
73 |
108 |
1.5 |
3.8e-15 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
348 |
430 |
1.2 |
1.1e-14 |
| c2.MILI_PSEUDOPODIA_HAPTOTAXIS_DN |
626 |
399 |
483 |
1.2 |
9.2e-14 |
| c5.GO_PROTEIN_COMPLEX_SUBUNIT_ORGANIZATI |
1299 |
827 |
947 |
1.1 |
1.1e-13 |
| c2.SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN |
223 |
142 |
189 |
1.3 |
1.7e-12 |
| c2.LU_AGING_BRAIN_UP |
239 |
152 |
199 |
1.3 |
1.5e-11 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANC |
397 |
253 |
313 |
1.2 |
2.6e-11 |
| c5.GO_ENDOPLASMIC_RETICULUM |
1285 |
818 |
924 |
1.1 |
4.4e-11 |
| c5.GO_ENDOPLASMIC_RETICULUM_PART |
926 |
590 |
679 |
1.2 |
7.9e-11 |
6_wk_FB_neuron-Fibroblast
| c2.REN_ALVEOLAR_RHABDOMYOSARCOMA_DN |
391 |
279 |
352 |
1.3 |
6.4e-20 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
873 |
992 |
1.1 |
3.3e-16 |
| CMC-modules_lightcyan |
268 |
191 |
243 |
1.3 |
4.7e-15 |
| c2.BLALOCK_ALZHEIMERS_DISEASE_UP |
1486 |
1059 |
1182 |
1.1 |
1.5e-14 |
| c5.GO_ENDOPLASMIC_RETICULUM |
1285 |
916 |
1027 |
1.1 |
1.0e-13 |
| c5.GO_ENDOPLASMIC_RETICULUM_PART |
926 |
660 |
752 |
1.1 |
5.4e-13 |
| c4.MODULE_1 |
318 |
227 |
278 |
1.2 |
3.4e-12 |
| c4.MODULE_47 |
196 |
140 |
178 |
1.3 |
1.6e-11 |
| c5.GO_MOVEMENT_OF_CELL_OR_SUBCELLULAR_CO |
951 |
678 |
765 |
1.1 |
1.6e-11 |
| c5.GO_LOCOMOTION |
785 |
560 |
636 |
1.1 |
8.5e-11 |
6_wk_FB_neuron-MEF
| c5.GO_POLY_A_RNA_BINDING |
1113 |
806 |
971 |
1.2 |
4.9e-35 |
| c5.GO_RNA_BINDING |
1466 |
1061 |
1240 |
1.2 |
5.2e-31 |
| c5.GO_RIBONUCLEOPROTEIN_COMPLEX |
660 |
478 |
595 |
1.2 |
2.0e-30 |
| c4.MODULE_83 |
308 |
223 |
297 |
1.3 |
3.5e-29 |
| pli_MID |
2881 |
2086 |
2313 |
1.1 |
3.2e-27 |
| c2.HSIAO_HOUSEKEEPING_GENES |
374 |
271 |
350 |
1.3 |
5.8e-26 |
| c4.MODULE_114 |
319 |
231 |
301 |
1.3 |
3.1e-24 |
| c5.GO_RIBONUCLEOPROTEIN_COMPLEX_BIOGENES |
419 |
303 |
384 |
1.3 |
2.3e-23 |
| c4.MODULE_151 |
298 |
216 |
281 |
1.3 |
1.5e-22 |
| c5.GO_RNA_PROCESSING |
781 |
565 |
674 |
1.2 |
1.4e-21 |
6_wk_FB_neuron-Myocyte
| c5.GO_RNA_BINDING |
1466 |
996 |
1243 |
1.2 |
1.4e-53 |
| c5.GO_POLY_A_RNA_BINDING |
1113 |
756 |
964 |
1.3 |
5.4e-50 |
| c5.GO_RIBONUCLEOPROTEIN_COMPLEX |
660 |
449 |
589 |
1.3 |
3.1e-39 |
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
1003 |
1215 |
1.2 |
6.5e-39 |
| CMC-modules_brown |
897 |
610 |
766 |
1.3 |
7.2e-35 |
| c4.MODULE_83 |
308 |
209 |
295 |
1.4 |
1.3e-34 |
| c5.GO_RNA_PROCESSING |
781 |
531 |
675 |
1.3 |
3.1e-34 |
| c4.MORF_UBE2I |
236 |
160 |
231 |
1.4 |
1.8e-32 |
| c4.MODULE_114 |
319 |
217 |
302 |
1.4 |
2.3e-32 |
| c4.MORF_CSNK2B |
286 |
194 |
274 |
1.4 |
2.7e-32 |
6_wk_FB_neuron-hiPSC
| c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED |
690 |
347 |
507 |
1.5 |
7.3e-37 |
| c2.MANALO_HYPOXIA_DN |
279 |
140 |
240 |
1.7 |
1.0e-36 |
| c5.GO_CHROMOSOME_ORGANIZATION |
875 |
441 |
614 |
1.4 |
1.5e-34 |
| c2.PUJANA_CHEK2_PCC_NETWORK |
730 |
368 |
522 |
1.4 |
9.8e-33 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
275 |
404 |
1.5 |
2.8e-30 |
| c5.GO_CHROMOSOME |
778 |
392 |
544 |
1.4 |
5.5e-30 |
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
743 |
949 |
1.3 |
6.1e-30 |
| c2.DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP |
304 |
153 |
244 |
1.6 |
1.1e-27 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_DN |
1224 |
616 |
797 |
1.3 |
1.5e-27 |
| c2.LEE_BMP2_TARGETS_DN |
826 |
416 |
564 |
1.4 |
6.8e-27 |
NPC-Astrocytes
| tissue_exp_brain |
495 |
320 |
402 |
1.3 |
2.2e-16 |
| secondary_FMRP-targets |
770 |
499 |
597 |
1.2 |
2.3e-15 |
| c5.GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMB |
998 |
646 |
731 |
1.1 |
1.9e-09 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
1000 |
647 |
730 |
1.1 |
5.2e-09 |
| c5.GO_REGULATION_OF_NEUROTRANSMITTER_LEV |
165 |
107 |
140 |
1.3 |
5.8e-09 |
| c5.GO_NEURON_PART |
1088 |
704 |
790 |
1.1 |
6.0e-09 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
793 |
883 |
1.1 |
7.5e-09 |
| c5.GO_SYNAPTIC_SIGNALING |
331 |
214 |
261 |
1.2 |
1.2e-08 |
| c2.BENPORATH_ES_WITH_H3K27ME3 |
730 |
473 |
541 |
1.1 |
1.8e-08 |
| c4.MODULE_66 |
474 |
307 |
361 |
1.2 |
3.5e-08 |
NPC-Neuron
| tissue_exp_brain |
495 |
279 |
399 |
1.4 |
5.9e-31 |
| c2.BENPORATH_ES_WITH_H3K27ME3 |
730 |
411 |
507 |
1.2 |
7.2e-14 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANC |
397 |
224 |
294 |
1.3 |
1.0e-13 |
| secondary_FMRP-targets |
770 |
434 |
528 |
1.2 |
7.2e-13 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
93 |
136 |
1.5 |
8.7e-13 |
| c2.BENPORATH_SUZ12_TARGETS |
664 |
374 |
455 |
1.2 |
3.5e-11 |
| CMC-modules_blue |
1154 |
650 |
754 |
1.2 |
6.6e-11 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
196 |
253 |
1.3 |
8.6e-11 |
| CMC-modules_red |
689 |
388 |
468 |
1.2 |
1.4e-10 |
| c5.GO_NEURON_PART |
1088 |
613 |
711 |
1.2 |
2.3e-10 |
NPC-Oligodendrocyte_Precursor_Cell
| secondary_FMRP-targets |
770 |
498 |
586 |
1.2 |
2.1e-12 |
| c5.GO_CELL_PROJECTION |
1508 |
976 |
1088 |
1.1 |
6.9e-11 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
1000 |
647 |
733 |
1.1 |
1.4e-09 |
| c5.GO_NEURON_PROJECTION |
835 |
540 |
614 |
1.1 |
1.4e-08 |
| c5.GO_VACUOLE |
959 |
621 |
699 |
1.1 |
1.6e-08 |
| c5.GO_GOLGI_APPARATUS |
1210 |
783 |
866 |
1.1 |
8.4e-08 |
| c5.GO_NEURON_PART |
1088 |
704 |
782 |
1.1 |
1.2e-07 |
| primary_PSD_(human_core) |
644 |
417 |
477 |
1.1 |
1.4e-07 |
| c2.BERENJENO_TRANSFORMED_BY_RHOA_DN |
365 |
236 |
281 |
1.2 |
2.1e-07 |
| c5.GO_CELL_SUBSTRATE_JUNCTION |
371 |
240 |
285 |
1.2 |
2.4e-07 |
NPC-Newly_Formed_Oligodendrocyte
| tissue_exp_brain |
495 |
284 |
415 |
1.5 |
1.7e-37 |
| c2.BENPORATH_ES_WITH_H3K27ME3 |
730 |
419 |
557 |
1.3 |
7.4e-28 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
199 |
283 |
1.4 |
4.0e-22 |
| c2.BENPORATH_SUZ12_TARGETS |
664 |
381 |
494 |
1.3 |
1.1e-20 |
| c2.MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 |
285 |
164 |
235 |
1.4 |
8.9e-20 |
| c2.BENPORATH_PRC2_TARGETS |
391 |
224 |
306 |
1.4 |
1.4e-18 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANC |
397 |
228 |
308 |
1.4 |
1.1e-17 |
| tissue_exp_testis |
452 |
259 |
342 |
1.3 |
1.6e-16 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
703 |
837 |
1.2 |
2.1e-16 |
| c5.GO_INTRINSIC_COMPONENT_OF_PLASMA_MEMB |
998 |
573 |
687 |
1.2 |
1.2e-14 |
NPC-Fibroblast
| c2.NABA_MATRISOME |
555 |
306 |
397 |
1.3 |
6.9e-16 |
| c2.WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216 |
297 |
164 |
230 |
1.4 |
7.1e-16 |
| Peptide_chain_elongation |
82 |
45 |
77 |
1.7 |
6.5e-15 |
| c2.REACTOME_PEPTIDE_CHAIN_ELONGATION |
84 |
46 |
78 |
1.7 |
2.4e-14 |
| Eukaryotic_Translation_Elongation |
84 |
46 |
78 |
1.7 |
2.4e-14 |
| Formation_of_a_pool_of_free_40S_subunit |
92 |
51 |
84 |
1.7 |
3.2e-14 |
| Viral_mRNA_Translation |
83 |
46 |
77 |
1.7 |
4.1e-14 |
| viral transcription |
82 |
45 |
76 |
1.7 |
6.9e-14 |
| c2.LEE_BMP2_TARGETS_UP |
598 |
330 |
417 |
1.3 |
9.2e-14 |
| 3’_-UTR-mediated_translational_regulati |
102 |
56 |
90 |
1.6 |
5.5e-13 |
NPC-MEF
| c4.MORF_RAD23A |
343 |
240 |
319 |
1.3 |
3.2e-26 |
| c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED |
690 |
483 |
599 |
1.2 |
3.6e-26 |
| c4.MORF_BUB3 |
275 |
193 |
261 |
1.4 |
1.4e-25 |
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
1034 |
1194 |
1.2 |
2.3e-23 |
| c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_U |
1176 |
824 |
967 |
1.2 |
2.7e-23 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
383 |
479 |
1.2 |
6.6e-23 |
| c4.MORF_CSNK2B |
286 |
200 |
266 |
1.3 |
4.6e-22 |
| c2.DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP |
1312 |
919 |
1061 |
1.2 |
1.2e-20 |
| c2.SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_U |
147 |
103 |
145 |
1.4 |
3.0e-20 |
| c2.KOBAYASHI_EGFR_SIGNALING_24HR_DN |
236 |
165 |
221 |
1.3 |
1.4e-19 |
NPC-Myocyte
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
754 |
1005 |
1.3 |
3.9e-44 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_DN |
1224 |
625 |
854 |
1.4 |
1.2e-43 |
| c2.PUJANA_CHEK2_PCC_NETWORK |
730 |
373 |
546 |
1.5 |
2.9e-41 |
| CMC-modules_black |
625 |
319 |
474 |
1.5 |
1.6e-38 |
| c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_U |
1176 |
600 |
810 |
1.3 |
4.7e-38 |
| c2.CAIRO_HEPATOBLASTOMA_CLASSES_UP |
581 |
297 |
434 |
1.5 |
1.2e-32 |
| c2.JOHNSTONE_PARVB_TARGETS_3_DN |
862 |
440 |
598 |
1.4 |
2.5e-29 |
| c2.RODRIGUES_THYROID_CARCINOMA_POORLY_DI |
604 |
308 |
440 |
1.4 |
6.5e-29 |
| c2.LEE_BMP2_TARGETS_DN |
826 |
422 |
575 |
1.4 |
7.9e-29 |
| c4.GNF2_EIF3S6 |
118 |
60 |
114 |
1.9 |
1.6e-28 |
NPC-hiPSC
| c2.PUJANA_BRCA1_PCC_NETWORK |
1476 |
850 |
1123 |
1.3 |
1.2e-54 |
| c2.KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_U |
1176 |
678 |
913 |
1.3 |
1.0e-50 |
| c2.PUJANA_CHEK2_PCC_NETWORK |
730 |
421 |
593 |
1.4 |
9.3e-44 |
| c2.GOBERT_OLIGODENDROCYTE_DIFFERENTIATIO |
547 |
315 |
460 |
1.5 |
1.1e-41 |
| c2.MARSON_BOUND_BY_E2F4_UNSTIMULATED |
690 |
398 |
559 |
1.4 |
1.4e-40 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_DN |
1224 |
705 |
914 |
1.3 |
2.4e-38 |
| c2.PUJANA_BRCA2_PCC_NETWORK |
388 |
224 |
337 |
1.5 |
9.6e-37 |
| c2.CAIRO_HEPATOBLASTOMA_CLASSES_UP |
581 |
335 |
473 |
1.4 |
2.0e-35 |
| Cell_Cycle |
455 |
262 |
382 |
1.5 |
2.1e-34 |
| h.HALLMARK_E2F_TARGETS |
199 |
115 |
188 |
1.6 |
1.5e-32 |
Analysis of original data



Analysis after correcting for cell type composition scores for fibroblasts and MEF



Color PCA by CTC score


Correlation of CTC scores with principal components

## Projected run time: ~ 2 min
## Projected run time: ~ 1 min
## [1] 0.02234939
## [1] 0.02350183
## [1] 0.003483011
##
## Wilcoxon signed rank test with continuity correction
##
## data: vpCellFrac2$Donor and vpCellFrac_minimal$Donor
## V = 40008000, p-value < 2.2e-16
## alternative hypothesis: true location shift is not equal to 0
all cell fractions

accounting for MEF and Fibroblast increases donor contributions
## Projected run time: ~ 1 min
## Projected run time: ~ 1 min
##
## Paired t-test
##
## data: df$adjusted and df$original
## t = 15.713, df = 18909, p-value < 2.2e-16
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
## 0.003048520 0.003917501
## sample estimates:
## mean of the differences
## 0.003483011
Percent bars

VariancePartition within each cell type

Compare donor effect

variancePartition: include technical variables
## Projected run time: ~ 4 min

Correlation between covariates

Differential expression between cases and controls in combined NPC + neuron dataset
Volcano plot

Genes with FDR < 30%
| ENSG00000230847 |
-3.8867431 |
-2.0458924 |
-7.503823 |
0.0000000 |
0.0000021 |
ENSG00000230847 |
| ENSG00000164930 |
-0.7773348 |
4.8643554 |
-5.911893 |
0.0000001 |
0.0008885 |
FZD6 |
| ENSG00000226259 |
-1.1458273 |
2.3980778 |
-5.496058 |
0.0000005 |
0.0032175 |
GTF2H2B |
| ENSG00000236725 |
-1.0340737 |
0.4658067 |
-5.316601 |
0.0000011 |
0.0040039 |
ENSG00000236725 |
| ENSG00000269337 |
-1.0984407 |
0.7260166 |
-5.313372 |
0.0000011 |
0.0040039 |
ENSG00000269337 |
| ENSG00000169629 |
-0.9328454 |
2.8967989 |
-4.990793 |
0.0000039 |
0.0118105 |
RGPD8 |
| ENSG00000184988 |
-0.6371885 |
0.6108187 |
-4.752049 |
0.0000097 |
0.0201639 |
TMEM106A |
| ENSG00000177873 |
-0.4751565 |
3.6251045 |
-4.744838 |
0.0000100 |
0.0201639 |
ZNF619 |
| ENSG00000145246 |
0.8099405 |
3.4869808 |
4.737294 |
0.0000103 |
0.0201639 |
ATP10D |
| ENSG00000121691 |
1.5711365 |
4.3941262 |
4.717053 |
0.0000111 |
0.0201639 |
CAT |
| ENSG00000003402 |
-1.2184673 |
2.9784138 |
-4.658510 |
0.0000138 |
0.0228447 |
CFLAR |
| ENSG00000173894 |
0.3974699 |
5.3493957 |
4.539741 |
0.0000215 |
0.0325994 |
CBX2 |
| ENSG00000237945 |
-1.4449894 |
3.0295611 |
-4.474223 |
0.0000273 |
0.0383219 |
LINC00649 |
| ENSG00000037757 |
-1.0264047 |
3.0641913 |
-4.421709 |
0.0000332 |
0.0408592 |
MRI1 |
| ENSG00000115828 |
-1.4442631 |
0.6431161 |
-4.417693 |
0.0000336 |
0.0408592 |
QPCT |
| ENSG00000181234 |
3.9832515 |
-0.9565400 |
4.375613 |
0.0000392 |
0.0446556 |
TMEM132C |
| ENSG00000164669 |
-0.9330823 |
-0.2461149 |
-4.356789 |
0.0000420 |
0.0450032 |
INTS4L1 |
| ENSG00000240342 |
-0.6669021 |
4.8380931 |
-4.336412 |
0.0000452 |
0.0457606 |
RPS2P5 |
| ENSG00000229404 |
-1.7586482 |
-0.9581430 |
-4.311301 |
0.0000495 |
0.0471821 |
LINC00858 |
| ENSG00000254353 |
-2.1384802 |
-0.4100724 |
-4.291721 |
0.0000531 |
0.0471821 |
ENSG00000254353 |
| ENSG00000226002 |
0.5981007 |
0.1750937 |
4.285220 |
0.0000544 |
0.0471821 |
ENSG00000226002 |
| ENSG00000244026 |
-0.5236215 |
3.8687373 |
-4.177683 |
0.0000799 |
0.0661458 |
FAM86DP |
| ENSG00000185985 |
2.7724325 |
5.1279631 |
4.162363 |
0.0000843 |
0.0668031 |
SLITRK2 |
| ENSG00000236383 |
-0.6271087 |
-0.4722674 |
-4.146970 |
0.0000891 |
0.0676050 |
LINC00854 |
| ENSG00000229789 |
-1.2992945 |
-0.2195011 |
-4.131695 |
0.0000940 |
0.0684996 |
ENSG00000229789 |
| ENSG00000010704 |
-0.9534242 |
-0.6692788 |
-4.104042 |
0.0001036 |
0.0717645 |
HFE |
| ENSG00000228463 |
-1.3430626 |
-0.4915192 |
-4.096619 |
0.0001064 |
0.0717645 |
ENSG00000228463 |
| ENSG00000115507 |
1.9964444 |
-0.0009156 |
4.075118 |
0.0001147 |
0.0733737 |
OTX1 |
| ENSG00000239959 |
-0.7577011 |
-0.1855192 |
-4.069923 |
0.0001168 |
0.0733737 |
ENPP7P2 |
| ENSG00000162618 |
-1.6783969 |
-0.7365519 |
-4.043841 |
0.0001279 |
0.0741853 |
ELTD1 |
| ENSG00000198715 |
-0.6225848 |
2.0519971 |
-4.037013 |
0.0001310 |
0.0741853 |
C1orf85 |
| ENSG00000107829 |
-0.5636433 |
1.8306642 |
-4.028719 |
0.0001349 |
0.0741853 |
FBXW4 |
| ENSG00000196569 |
-1.2655757 |
3.3493015 |
-4.027240 |
0.0001356 |
0.0741853 |
LAMA2 |
| ENSG00000221870 |
2.5063090 |
1.4534521 |
4.021192 |
0.0001385 |
0.0741853 |
TMEM257 |
| ENSG00000227775 |
0.4286190 |
4.0581385 |
3.993127 |
0.0001526 |
0.0794408 |
ENSG00000227775 |
| ENSG00000160789 |
-0.3087472 |
6.1850559 |
-3.945999 |
0.0001796 |
0.0896624 |
LMNA |
| ENSG00000212719 |
-2.8235614 |
2.0022500 |
-3.938600 |
0.0001842 |
0.0896624 |
C17orf51 |
| ENSG00000259085 |
0.4518444 |
0.8237710 |
3.934224 |
0.0001870 |
0.0896624 |
ENSG00000259085 |
| ENSG00000137962 |
-0.8405123 |
5.9505584 |
-3.925476 |
0.0001927 |
0.0900281 |
ARHGAP29 |
| ENSG00000148942 |
-1.7992311 |
-0.7765750 |
-3.905677 |
0.0002063 |
0.0939415 |
SLC5A12 |
| ENSG00000234431 |
-1.1610396 |
-0.0453674 |
-3.836649 |
0.0002609 |
0.1159417 |
ENSG00000234431 |
| ENSG00000106868 |
-0.4221252 |
5.3831940 |
-3.801357 |
0.0002940 |
0.1275207 |
SUSD1 |
| ENSG00000256043 |
-1.1396397 |
2.1885944 |
-3.734748 |
0.0003676 |
0.1502070 |
CTSO |
| ENSG00000183036 |
1.0568761 |
0.2824591 |
3.731252 |
0.0003719 |
0.1502070 |
PCP4 |
| ENSG00000255983 |
-1.7770246 |
-1.6255799 |
-3.724899 |
0.0003799 |
0.1502070 |
ENSG00000255983 |
| ENSG00000108946 |
-0.1539076 |
8.5710566 |
-3.720296 |
0.0003857 |
0.1502070 |
PRKAR1A |
| ENSG00000118946 |
-0.6964719 |
6.9945080 |
-3.710494 |
0.0003985 |
0.1502070 |
PCDH17 |
| ENSG00000146833 |
-1.7925956 |
2.0933749 |
-3.708006 |
0.0004018 |
0.1502070 |
TRIM4 |
| ENSG00000238286 |
0.3957608 |
0.6291523 |
3.706382 |
0.0004040 |
0.1502070 |
SLC35E1P1 |
| ENSG00000234719 |
-0.9946496 |
0.9947928 |
-3.679553 |
0.0004416 |
0.1608973 |
ENSG00000234719 |
| ENSG00000222489 |
0.4179907 |
0.2003903 |
3.668398 |
0.0004582 |
0.1613770 |
ENSG00000222489 |
| ENSG00000145736 |
-0.5293506 |
3.2139470 |
-3.666787 |
0.0004606 |
0.1613770 |
GTF2H2 |
| ENSG00000234171 |
-0.3666779 |
2.5715243 |
-3.646265 |
0.0004929 |
0.1694146 |
ENSG00000234171 |
| ENSG00000263535 |
-0.5471106 |
0.2504930 |
-3.637930 |
0.0005066 |
0.1696258 |
AK4P1 |
| ENSG00000105963 |
-0.5320618 |
0.9723243 |
-3.629585 |
0.0005206 |
0.1696258 |
ADAP1 |
| ENSG00000185518 |
-1.4407644 |
-0.7248376 |
-3.629134 |
0.0005214 |
0.1696258 |
SV2B |
| ENSG00000136104 |
0.3501590 |
3.8369805 |
3.609525 |
0.0005560 |
0.1735517 |
RNASEH2B |
| ENSG00000232300 |
0.5848956 |
-0.3102700 |
3.597250 |
0.0005788 |
0.1735517 |
FAM215B |
| ENSG00000266937 |
-0.2438614 |
1.6488055 |
-3.592392 |
0.0005880 |
0.1735517 |
ENSG00000266937 |
| ENSG00000198932 |
-0.5232759 |
4.2805161 |
-3.590830 |
0.0005910 |
0.1735517 |
GPRASP1 |
| ENSG00000105971 |
-0.4935931 |
4.8915284 |
-3.586868 |
0.0005987 |
0.1735517 |
CAV2 |
| ENSG00000066382 |
1.6313657 |
3.2008651 |
3.586588 |
0.0005993 |
0.1735517 |
MPPED2 |
| ENSG00000169436 |
2.9415822 |
-1.3911095 |
3.586128 |
0.0006002 |
0.1735517 |
COL22A1 |
| ENSG00000022556 |
2.4000333 |
1.2777887 |
3.576075 |
0.0006201 |
0.1765254 |
NLRP2 |
| ENSG00000227318 |
-1.7281778 |
-0.6086402 |
-3.568752 |
0.0006351 |
0.1772296 |
ENSG00000227318 |
| ENSG00000170089 |
-0.4997211 |
2.3869475 |
-3.565386 |
0.0006421 |
0.1772296 |
ENSG00000170089 |
| ENSG00000196993 |
-0.7658407 |
0.0667859 |
-3.556916 |
0.0006600 |
0.1794504 |
NPIPB9 |
| ENSG00000217512 |
0.3593747 |
0.6649783 |
3.523761 |
0.0007347 |
0.1968282 |
ENSG00000217512 |
| ENSG00000036448 |
0.7667332 |
1.7145378 |
3.512307 |
0.0007623 |
0.1976310 |
MYOM2 |
| ENSG00000141837 |
-1.0014302 |
1.3880998 |
-3.507836 |
0.0007733 |
0.1976310 |
CACNA1A |
| ENSG00000269600 |
1.6893815 |
-1.3032529 |
3.507404 |
0.0007744 |
0.1976310 |
ENSG00000269600 |
| ENSG00000169955 |
-0.6639366 |
1.6450844 |
-3.504748 |
0.0007811 |
0.1976310 |
ZNF747 |
| ENSG00000176978 |
-0.4750891 |
3.9911880 |
-3.496565 |
0.0008019 |
0.2001168 |
DPP7 |
| ENSG00000146707 |
-0.3052560 |
3.3309046 |
-3.484563 |
0.0008333 |
0.2051604 |
POMZP3 |
| ENSG00000126822 |
0.9815936 |
4.3171322 |
3.470810 |
0.0008708 |
0.2115342 |
PLEKHG3 |
| ENSG00000253954 |
0.8588332 |
-0.0100037 |
3.449438 |
0.0009323 |
0.2222635 |
HMGN1P38 |
| ENSG00000011405 |
0.1496642 |
7.6232380 |
3.447050 |
0.0009394 |
0.2222635 |
PIK3C2A |
| ENSG00000105136 |
-0.1753927 |
4.7028745 |
-3.438130 |
0.0009665 |
0.2257293 |
ZNF419 |
| ENSG00000128591 |
-0.9814583 |
5.8216396 |
-3.401220 |
0.0010863 |
0.2505191 |
FLNC |
| ENSG00000153406 |
0.5476832 |
1.1225174 |
3.392704 |
0.0011159 |
0.2541254 |
NMRAL1 |
| ENSG00000259363 |
0.7834232 |
0.2059661 |
3.382747 |
0.0011515 |
0.2551405 |
ENSG00000259363 |
| ENSG00000261520 |
1.3416498 |
0.5496398 |
3.381676 |
0.0011554 |
0.2551405 |
DLGAP1-AS5 |
| ENSG00000175548 |
-0.5063777 |
4.4022251 |
-3.376397 |
0.0011747 |
0.2551405 |
ALG10B |
| ENSG00000185760 |
1.5278096 |
-0.4446505 |
3.375886 |
0.0011766 |
0.2551405 |
KCNQ5 |
| ENSG00000151834 |
2.3592184 |
-1.6572592 |
3.372175 |
0.0011904 |
0.2551405 |
GABRA2 |
| ENSG00000188107 |
0.4359750 |
3.0692274 |
3.334455 |
0.0013396 |
0.2787115 |
EYS |
| ENSG00000048462 |
-1.2491868 |
-0.2793089 |
-3.333326 |
0.0013444 |
0.2787115 |
TNFRSF17 |
| ENSG00000136842 |
-0.8606898 |
1.1975239 |
-3.332867 |
0.0013463 |
0.2787115 |
TMOD1 |
| ENSG00000170876 |
-0.1548197 |
6.2213758 |
-3.308470 |
0.0014525 |
0.2913382 |
TMEM43 |
| ENSG00000226869 |
1.9505848 |
-1.0381730 |
3.308194 |
0.0014537 |
0.2913382 |
LHFPL3-AS1 |
| ENSG00000185149 |
-1.2408556 |
0.7281455 |
-3.307857 |
0.0014552 |
0.2913382 |
NPY2R |
| ENSG00000203504 |
0.6387076 |
-0.3051535 |
3.299804 |
0.0014921 |
0.2954617 |
ENSG00000203504 |
| ENSG00000187667 |
-0.8113413 |
-0.1035667 |
-3.291976 |
0.0015287 |
0.2994599 |
WHAMMP3 |
Differential expression within each cell type

Gene set tests
NPC - roast
| regulation of oxidoreductase activity |
45 |
0.0888889 |
0.0000000 |
Down |
0.0084 |
0.9875099 |
0.7411 |
0.9949959 |
| c2.MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP |
18 |
0.1666667 |
0.0000000 |
Down |
0.0094 |
0.9875099 |
0.2390 |
0.9949959 |
| regulation of monooxygenase activity |
32 |
0.1250000 |
0.0000000 |
Down |
0.0098 |
0.9875099 |
0.5790 |
0.9949959 |
| abnormal_interleukin-1_beta_secretion |
28 |
0.2142857 |
0.0000000 |
Down |
0.0119 |
0.9875099 |
0.2290 |
0.9949959 |
| regulation of nitric-oxide synthase activity |
28 |
0.1428571 |
0.0000000 |
Down |
0.0125 |
0.9875099 |
0.4739 |
0.9949959 |
| increased_interleukin-1_beta_secretion |
16 |
0.2500000 |
0.0000000 |
Down |
0.0142 |
0.9875099 |
0.1628 |
0.9949959 |
| decreased_susceptibility_to_viral_infection |
25 |
0.2000000 |
0.0000000 |
Down |
0.0146 |
0.9875099 |
0.5284 |
0.9949959 |
| c5.GO_MYOFILAMENT |
13 |
0.2307692 |
0.0000000 |
Down |
0.0147 |
0.9875099 |
0.1813 |
0.9949959 |
| c5.GO_REGULATION_OF_KERATINOCYTE_PROLIFERATION |
18 |
0.1111111 |
0.2222222 |
Up |
0.0156 |
0.9875099 |
0.1292 |
0.9949959 |
| c4.GNF2_MYD88 |
43 |
0.2790698 |
0.0232558 |
Down |
0.0168 |
0.9875099 |
0.1240 |
0.9949959 |
| metalloexopeptidase activity |
27 |
0.2222222 |
0.0000000 |
Down |
0.0192 |
0.9875099 |
0.4459 |
0.9949959 |
| c2.TAVOR_CEBPA_TARGETS_DN |
23 |
0.1304348 |
0.0434783 |
Down |
0.0202 |
0.9875099 |
0.5067 |
0.9949959 |
| c7.GSE13887_HEALTHY_VS_LUPUS_RESTING_CD4_TCELL_UP |
75 |
0.1066667 |
0.0400000 |
Down |
0.0202 |
0.9875099 |
0.4062 |
0.9949959 |
| c4.GNF2_VAV1 |
23 |
0.2608696 |
0.0000000 |
Down |
0.0207 |
0.9875099 |
0.3512 |
0.9949959 |
| c5.GO_GABA_RECEPTOR_ACTIVITY |
11 |
0.0000000 |
0.3636364 |
Up |
0.0208 |
0.9875099 |
0.0526 |
0.9949959 |
| abnormal_interleukin-1_secretion |
29 |
0.2068966 |
0.0000000 |
Down |
0.0211 |
0.9875099 |
0.2368 |
0.9949959 |
| c4.GCM_PRKCG |
42 |
0.0714286 |
0.0000000 |
Down |
0.0212 |
0.9875099 |
0.7766 |
0.9949959 |
| c5.GO_REGULATION_OF_OXIDOREDUCTASE_ACTIVITY |
63 |
0.0634921 |
0.0000000 |
Down |
0.0212 |
0.9875099 |
0.8457 |
0.9949959 |
| c5.GO_REGULATION_OF_LYMPHOCYTE_MIGRATION |
15 |
0.2666667 |
0.0666667 |
Down |
0.0218 |
0.9875099 |
0.1153 |
0.9949959 |
| c5.GO_METALLOEXOPEPTIDASE_ACTIVITY |
33 |
0.1515152 |
0.0000000 |
Down |
0.0223 |
0.9875099 |
0.5898 |
0.9949959 |
NPC - romer
| tissue_exp_spleen |
11 |
0.322810 |
0.677215 |
0.000009 |
| c6.P53_DN.V1_UP |
156 |
0.863625 |
0.136381 |
0.000026 |
| c7.GSE5589_WT_VS_IL10_KO_LPS_AND_IL10_STIM_MACROPHAGE_180MIN_DN |
74 |
0.211088 |
0.788918 |
0.000079 |
| abnormal_cellular_extravasation |
21 |
0.997517 |
0.002485 |
0.000088 |
| c7.GSE17974_CTRL_VS_ACT_IL4_AND_ANTI_IL12_0.5H_CD4_TCELL_UP |
100 |
0.677260 |
0.322749 |
0.000102 |
| neuropeptide receptor activity |
16 |
0.411699 |
0.588317 |
0.000142 |
| c7.GSE21546_WT_VS_ELK1_KO_DP_THYMOCYTES_UP |
169 |
0.911123 |
0.088881 |
0.000197 |
| c2.MIKKELSEN_MCV6_LCP_WITH_H3K4ME3 |
93 |
0.849840 |
0.150164 |
0.000249 |
| c2.AIGNER_ZEB1_TARGETS |
21 |
0.377884 |
0.622127 |
0.000404 |
| c5.GO_NEUROPEPTIDE_RECEPTOR_ACTIVITY |
16 |
0.275191 |
0.724821 |
0.000486 |
| c5.GO_REGULATION_OF_NITRIC_OXIDE_BIOSYNTHETIC_PROCESS |
36 |
0.993441 |
0.006562 |
0.000495 |
| c2.MIKKELSEN_ES_HCP_WITH_H3K27ME3 |
28 |
0.072571 |
0.927434 |
0.000584 |
| c5.GO_APICAL_PLASMA_MEMBRANE |
192 |
0.593364 |
0.406641 |
0.000609 |
| neurotransmitter receptor activity |
39 |
0.177289 |
0.822723 |
0.000660 |
| G-protein coupled amine receptor activity |
15 |
0.034149 |
0.965857 |
0.000676 |
| abnormal_aggression-related_behavior |
56 |
0.176260 |
0.823751 |
0.000682 |
| regulation of endocytosis |
93 |
0.766329 |
0.233676 |
0.000692 |
| c7.GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP |
162 |
0.968249 |
0.031755 |
0.000804 |
| c7.GSE23114_WT_VS_SLE2C1_MOUSE_PERITONEAL_CAVITY_B1A_BCELL_DN |
117 |
0.037731 |
0.962272 |
0.000819 |
| KEGG_AFRICAN_TRYPANOSOMIASIS |
16 |
0.957646 |
0.042361 |
0.000819 |
Neuron - roast
| c2.ONO_FOXP3_TARGETS_UP |
15 |
0.4666667 |
0.0000000 |
Down |
0.0006 |
0.5300318 |
0.0603 |
0.7084585 |
| c7.GSE21927_SPLENIC_C26GM_TUMOROUS_VS_4T1_TUMOR_MONOCYTES_UP |
126 |
0.1666667 |
0.0317460 |
Down |
0.0008 |
0.5300318 |
0.3194 |
0.7084585 |
| atc.level3-new_ARTERIOLAR_SMOOTH_MUSCLE_AGENTS_ACTING_ON |
24 |
0.1666667 |
0.0000000 |
Down |
0.0009 |
0.5300318 |
0.1127 |
0.7084585 |
| c5.GO_MYOFILAMENT |
13 |
0.2307692 |
0.0000000 |
Down |
0.0014 |
0.5300318 |
0.0542 |
0.7084585 |
| c7.GSE12505_WT_VS_E2-2_HET_PDC_UP |
82 |
0.1341463 |
0.0121951 |
Down |
0.0014 |
0.5300318 |
0.4324 |
0.7084585 |
| thymus_atrophy |
36 |
0.2777778 |
0.0277778 |
Down |
0.0016 |
0.5300318 |
0.0571 |
0.7084585 |
| c5.GO_REGULATION_OF_REACTIVE_OXYGEN_SPECIES_BIOSYNTHETIC_PROCESS |
47 |
0.2340426 |
0.0425532 |
Down |
0.0018 |
0.5300318 |
0.1157 |
0.7084585 |
| c7.GSE17301_IFNA2_VS_IFNA2_AND_ACD3_ACD28_STIM_CD8_TCELL_DN |
161 |
0.1552795 |
0.0310559 |
Down |
0.0018 |
0.5300318 |
0.2752 |
0.7084585 |
| c7.GSE11961_FOLLICULAR_BCELL_VS_MEMORY_BCELL_DAY40_DN |
167 |
0.1437126 |
0.0239521 |
Down |
0.0020 |
0.5300318 |
0.3445 |
0.7084585 |
| c5.GO_ACTIN_MYOSIN_FILAMENT_SLIDING |
18 |
0.2777778 |
0.0555556 |
Down |
0.0021 |
0.5300318 |
0.0551 |
0.7084585 |
| c2.WIKMAN_ASBESTOS_LUNG_CANCER_DN |
21 |
0.2380952 |
0.0476190 |
Down |
0.0021 |
0.5300318 |
0.2568 |
0.7084585 |
| gws3k-8.6_Bipolar_disorder |
33 |
0.1515152 |
0.0606061 |
Down |
0.0023 |
0.5300318 |
0.1640 |
0.7084585 |
| muscle filament sliding |
18 |
0.2777778 |
0.0555556 |
Down |
0.0024 |
0.5300318 |
0.0542 |
0.7084585 |
| positive regulation of interleukin-12 production |
9 |
0.3333333 |
0.0000000 |
Down |
0.0026 |
0.5300318 |
0.0604 |
0.7084585 |
| actin-myosin filament sliding |
18 |
0.2777778 |
0.0555556 |
Down |
0.0026 |
0.5300318 |
0.0555 |
0.7084585 |
| c2.KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION |
22 |
0.2272727 |
0.0000000 |
Down |
0.0030 |
0.5300318 |
0.2609 |
0.7084585 |
| c5.GO_MUSCLE_FILAMENT_SLIDING |
18 |
0.2777778 |
0.0555556 |
Down |
0.0031 |
0.5300318 |
0.0539 |
0.7084585 |
| c7.GSE13887_ACT_CD4_VS_NO_TREATED_CD4_TCELL_DN |
74 |
0.1621622 |
0.0270270 |
Down |
0.0036 |
0.5300318 |
0.1902 |
0.7084585 |
| c5.GO_POSITIVE_REGULATION_OF_MYELOID_LEUKOCYTE_DIFFERENTIATION |
31 |
0.2580645 |
0.0000000 |
Down |
0.0037 |
0.5300318 |
0.4136 |
0.7084585 |
| c7.GSE15324_NAIVE_VS_ACTIVATED_ELF4_KO_CD8_TCELL_UP |
172 |
0.1046512 |
0.0465116 |
Down |
0.0037 |
0.5300318 |
0.4801 |
0.7084585 |
Neuron - romer
| small_cranium |
22 |
0.881040 |
0.118974 |
0.000209 |
| abnormal_neutrophil_physiology |
63 |
0.948462 |
0.051540 |
0.000315 |
| c2.REACTOME_FRS2_MEDIATED_CASCADE |
24 |
0.871439 |
0.128572 |
0.000463 |
| c5.GO_RECEPTOR_SIGNALING_COMPLEX_SCAFFOLD_ACTIVITY |
21 |
0.622760 |
0.377261 |
0.000472 |
| c5.GO_BITTER_TASTE_RECEPTOR_ACTIVITY |
13 |
0.000485 |
0.999517 |
0.000975 |
| c7.GSE7831_UNSTIM_VS_CPG_STIM_PDC_4H_DN |
164 |
0.965137 |
0.034866 |
0.000978 |
| c7.GSE3203_INFLUENZA_INF_VS_IFNB_TREATED_LN_BCELL_UP |
148 |
0.954974 |
0.045032 |
0.001123 |
| c2.ST_GA13_PATHWAY |
33 |
0.943450 |
0.056554 |
0.001164 |
| c2.REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION |
10 |
0.358605 |
0.641422 |
0.001214 |
| FGFR_ligand_binding_and_activation |
10 |
0.358605 |
0.641422 |
0.001214 |
| c2.BIOCARTA_DC_PATHWAY |
2 |
0.493295 |
0.506809 |
0.001221 |
| BIOCARTA_DC_PATHWAY |
2 |
0.493295 |
0.506809 |
0.001221 |
| c2.KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP |
37 |
0.992855 |
0.007148 |
0.001245 |
| FRS2-mediated_cascade |
25 |
0.858513 |
0.141496 |
0.001300 |
| c5.GO_CELLULAR_CARBOHYDRATE_BIOSYNTHETIC_PROCESS |
44 |
0.984485 |
0.015517 |
0.001397 |
| c5.GO_POLYOL_BIOSYNTHETIC_PROCESS |
22 |
0.921682 |
0.078323 |
0.001402 |
| c5.GO_REGULATION_OF_SYSTEMIC_ARTERIAL_BLOOD_PRESSURE_BY_RENIN_ANGIOTENSIN |
10 |
0.674343 |
0.325686 |
0.001404 |
| decreased_cranium_height |
23 |
0.966559 |
0.033446 |
0.001502 |
| c5.GO_LIPOPROTEIN_PARTICLE_RECEPTOR_BINDING |
15 |
0.939037 |
0.060972 |
0.001834 |
| abnormal_cranium_size |
55 |
0.901358 |
0.098649 |
0.001864 |
Compare logFC between celltypes


Genes with FDR < 30% within NPC or neuron separately
Neuron
| ENSG00000230847 |
-4.1176470 |
-2.0458924 |
-6.121625 |
0.00e+00 |
0.0008056 |
ENSG00000230847 |
| ENSG00000173894 |
0.5551547 |
5.3493957 |
4.617878 |
1.63e-05 |
0.1543658 |
CBX2 |
| ENSG00000115828 |
-1.7332719 |
0.6431161 |
-4.505460 |
2.47e-05 |
0.1560023 |
QPCT |
| ENSG00000164669 |
-1.2307287 |
-0.2461149 |
-4.337493 |
4.56e-05 |
0.2158049 |
INTS4L1 |
| ENSG00000164930 |
-0.7391163 |
4.8643554 |
-4.248241 |
6.29e-05 |
0.2378761 |
FZD6 |
NPC
| ENSG00000230847 |
-3.5818061 |
-2.0458924 |
-5.077991 |
2.80e-06 |
0.0536223 |
ENSG00000230847 |
| ENSG00000226259 |
-1.2943834 |
2.3980778 |
-4.621129 |
1.61e-05 |
0.1046486 |
GTF2H2B |
| ENSG00000164930 |
-0.8172728 |
4.8643554 |
-4.613377 |
1.66e-05 |
0.1046486 |
FZD6 |
| ENSG00000162618 |
-2.3869758 |
-0.7365519 |
-4.429296 |
3.27e-05 |
0.1546567 |
ELTD1 |
| ENSG00000236725 |
-1.1055833 |
0.4658067 |
-4.236436 |
6.56e-05 |
0.2481135 |
ENSG00000236725 |
Effect of correcting for Fibroblast score on case-control t-statistics in NPCs
We have demonstrated that correcting for the fibroblast score is important, especially in boosting concordance with HBCC. So what genes are affected by this correction? In order to test this, I compared the absolute value of the t-statstic (the test-statistic used compute the p-value) from the adjusted and unadjusted test.
| c2.REACTOME_RNA_POL_I_PROMOTER_OPENING |
53 |
3.11 |
22 |
7.07 |
5.205652e-14 |
| c2.REACTOME_AMYLOIDS |
61 |
3.58 |
23 |
6.42 |
1.630978e-13 |
| KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
79 |
4.64 |
26 |
5.60 |
1.805959e-13 |
| c2.KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
80 |
4.70 |
26 |
5.53 |
2.528446e-13 |
| kegg_Systemic_lupus_erythematosus |
80 |
4.70 |
26 |
5.53 |
2.528446e-13 |
| c5.GO_DNA_PACKAGING_COMPLEX |
80 |
4.70 |
25 |
5.32 |
1.977977e-12 |
| c2.REACTOME_PACKAGING_OF_TELOMERE_ENDS |
41 |
2.41 |
18 |
7.48 |
3.281350e-12 |
| KEGG_ALCOHOLISM |
149 |
8.75 |
34 |
3.89 |
5.041777e-12 |
| kegg_Alcoholism |
149 |
8.75 |
34 |
3.89 |
5.041777e-12 |
| CMC-modules_forestgreen |
28 |
1.64 |
15 |
9.12 |
5.556191e-12 |
| c2.REACTOME_RNA_POL_I_TRANSCRIPTION |
78 |
4.58 |
24 |
5.24 |
7.968194e-12 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
9.69 |
35 |
3.61 |
2.248728e-11 |
| c2.REACTOME_MEIOTIC_RECOMBINATION |
71 |
4.17 |
22 |
5.28 |
5.078763e-11 |
| c2.REACTOME_MEIOSIS |
95 |
5.58 |
24 |
4.30 |
7.564072e-10 |
| c2.REACTOME_TELOMERE_MAINTENANCE |
67 |
3.93 |
20 |
5.08 |
8.074538e-10 |
up only
| secondary_FMRP-targets |
770 |
22.64 |
55 |
2.43 |
8.964789e-10 |
| c2.KIM_ALL_DISORDERS_CALB1_CORR_UP |
517 |
15.20 |
42 |
2.76 |
2.518142e-09 |
| CMC-modules_red |
689 |
20.25 |
48 |
2.37 |
2.541420e-08 |
| c5.GO_CELL_PROJECTION |
1508 |
44.33 |
80 |
1.80 |
1.172295e-07 |
| c5.GO_CELL_PROJECTION_PART |
809 |
23.78 |
51 |
2.14 |
2.186483e-07 |
| c5.GO_SYNAPSE |
677 |
19.90 |
45 |
2.26 |
2.751798e-07 |
| kirov_psych.ed.set_mGluR5 |
37 |
1.09 |
9 |
8.27 |
9.066695e-07 |
| kirov_synaptic.sets_mGluR5 |
37 |
1.09 |
9 |
8.27 |
9.066695e-07 |
| primary_mGluR5 |
37 |
1.09 |
9 |
8.27 |
9.066695e-07 |
| c2.WANG_LSD1_TARGETS_DN |
31 |
0.91 |
8 |
8.78 |
2.282486e-06 |
| primary_PSD_(human_core) |
644 |
18.93 |
41 |
2.17 |
2.852382e-06 |
| c5.GO_CYTOSKELETAL_PROTEIN_BINDING |
693 |
20.37 |
43 |
2.11 |
3.130646e-06 |
| cav2_Cav2::ALL |
193 |
5.67 |
19 |
3.35 |
4.282863e-06 |
| c2.BLALOCK_ALZHEIMERS_DISEASE_DN |
1184 |
34.81 |
62 |
1.78 |
5.870449e-06 |
| c4.MODULE_100 |
467 |
13.73 |
32 |
2.33 |
8.398773e-06 |
downonly
| c2.REACTOME_RNA_POL_I_PROMOTER_OPENING |
53 |
1.55 |
22 |
14.15 |
2.321068e-20 |
| c2.REACTOME_AMYLOIDS |
61 |
1.79 |
23 |
12.85 |
4.358139e-20 |
| KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
79 |
2.32 |
25 |
10.79 |
1.461924e-19 |
| c2.KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS |
80 |
2.35 |
25 |
10.65 |
2.069585e-19 |
| c5.GO_DNA_PACKAGING_COMPLEX |
80 |
2.35 |
25 |
10.65 |
2.069585e-19 |
| kegg_Systemic_lupus_erythematosus |
80 |
2.35 |
25 |
10.65 |
2.069585e-19 |
| c2.REACTOME_RNA_POL_I_TRANSCRIPTION |
78 |
2.29 |
23 |
10.05 |
2.526080e-17 |
| c2.REACTOME_MEIOTIC_RECOMBINATION |
71 |
2.08 |
22 |
10.56 |
3.831306e-17 |
| CMC-modules_forestgreen |
28 |
0.82 |
15 |
18.26 |
2.155808e-16 |
| KEGG_ALCOHOLISM |
149 |
4.37 |
29 |
6.64 |
3.733569e-16 |
| kegg_Alcoholism |
149 |
4.37 |
29 |
6.64 |
3.733569e-16 |
| c5.GO_PROTEIN_DNA_COMPLEX |
141 |
4.14 |
27 |
6.53 |
6.093019e-15 |
| c5.GO_NEGATIVE_REGULATION_OF_GENE_EXPRESSION_EPIGENETIC |
89 |
2.61 |
22 |
8.43 |
7.612436e-15 |
| c2.REACTOME_PACKAGING_OF_TELOMERE_ENDS |
41 |
1.20 |
16 |
13.30 |
1.218042e-14 |
| c5.GO_CHROMATIN_SILENCING |
73 |
2.14 |
20 |
9.34 |
1.509248e-14 |

Effect of correcting for Fibroblast score on case-control t-statistics in Neurons
| tissue_exp_brain |
495 |
29.13 |
85 |
2.92 |
1.703722e-19 |
| CMC-modules_red |
689 |
40.55 |
89 |
2.19 |
1.306218e-12 |
| c5.GO_SYNAPSE_PART |
549 |
32.31 |
74 |
2.29 |
1.522632e-11 |
| c5.GO_SYNAPSE |
677 |
39.85 |
85 |
2.13 |
1.977615e-11 |
| h.HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
177 |
10.42 |
36 |
3.46 |
4.439413e-11 |
| c5.GO_NEURON_PART |
1088 |
64.04 |
117 |
1.83 |
7.934100e-11 |
| c4.MODULE_47 |
196 |
11.54 |
37 |
3.21 |
2.288108e-10 |
| secondary_FMRP-targets |
770 |
45.32 |
90 |
1.99 |
2.311185e-10 |
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
9.71 |
33 |
3.40 |
4.544049e-10 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
20.42 |
51 |
2.50 |
1.252737e-09 |
| c5.GO_PRESYNAPTIC_PROCESS_INVOLVED_IN_SYNAPTIC_TRANSMISSION |
101 |
5.94 |
24 |
4.04 |
3.009981e-09 |
| c2.MEISSNER_NPC_HCP_WITH_H3K4ME2 |
390 |
22.95 |
54 |
2.35 |
3.612506e-09 |
| c5.GO_NEURON_PROJECTION |
835 |
49.15 |
91 |
1.85 |
6.490311e-09 |
| abnormal_motor_coordination_balance |
458 |
26.96 |
59 |
2.19 |
1.054544e-08 |
| c5.GO_NEUROTRANSMITTER_TRANSPORT |
133 |
7.83 |
27 |
3.45 |
1.239876e-08 |
up only
| c2.KIM_ALL_DISORDERS_CALB1_CORR_UP |
517 |
15.10 |
46 |
3.05 |
1.583029e-11 |
| CMC-modules_red |
689 |
20.12 |
54 |
2.68 |
3.329240e-11 |
| tissue_exp_brain |
495 |
14.46 |
43 |
2.97 |
1.630936e-10 |
| secondary_FMRP-targets |
770 |
22.49 |
52 |
2.31 |
1.434069e-08 |
| c2.BLALOCK_ALZHEIMERS_DISEASE_DN |
1184 |
34.58 |
68 |
1.97 |
5.070287e-08 |
| c5.GO_SYNAPSE |
677 |
19.77 |
46 |
2.33 |
8.738854e-08 |
| c5.GO_PRESYNAPTIC_PROCESS_INVOLVED_IN_SYNAPTIC_TRANSMISSION |
101 |
2.95 |
15 |
5.09 |
2.271475e-07 |
| c5.GO_SYNAPSE_PART |
549 |
16.03 |
39 |
2.43 |
2.879986e-07 |
| c4.MODULE_100 |
467 |
13.64 |
35 |
2.57 |
3.434816e-07 |
| primary_PSD_(human_core) |
644 |
18.81 |
43 |
2.29 |
3.811836e-07 |
| c4.MODULE_66 |
474 |
13.84 |
35 |
2.53 |
4.881700e-07 |
| kirov_psych.ed.set_mGluR5 |
37 |
1.08 |
9 |
8.33 |
8.584918e-07 |
| kirov_synaptic.sets_mGluR5 |
37 |
1.08 |
9 |
8.33 |
8.584918e-07 |
| primary_mGluR5 |
37 |
1.08 |
9 |
8.33 |
8.584918e-07 |
| c2.REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES |
159 |
4.64 |
18 |
3.88 |
9.357542e-07 |
downonly
| c2.VERHAAK_GLIOBLASTOMA_PRONEURAL |
165 |
4.89 |
23 |
4.70 |
6.649058e-10 |
| tissue_exp_brain |
495 |
14.68 |
42 |
2.86 |
8.851474e-10 |
| c2.WONG_ADULT_TISSUE_STEM_MODULE |
591 |
17.52 |
46 |
2.62 |
2.189234e-09 |
| h.HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
177 |
5.25 |
22 |
4.19 |
1.376309e-08 |
| c2.MIKKELSEN_MEF_HCP_WITH_H3K27ME3 |
347 |
10.29 |
31 |
3.01 |
4.817120e-08 |
| c2.SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN |
223 |
6.61 |
24 |
3.63 |
5.156047e-08 |
| c2.CUI_TCF21_TARGETS_2_DN |
744 |
22.06 |
50 |
2.27 |
5.305225e-08 |
| c5.GO_NEURON_PART |
1088 |
32.26 |
64 |
1.98 |
9.817372e-08 |
| c2.DODD_NASOPHARYNGEAL_CARCINOMA_UP |
1225 |
36.32 |
69 |
1.90 |
1.538746e-07 |
| c5.GO_LEUKOCYTE_MEDIATED_IMMUNITY |
94 |
2.79 |
14 |
5.02 |
6.656525e-07 |
| c5.GO_LYMPHOCYTE_MEDIATED_IMMUNITY |
69 |
2.05 |
12 |
5.86 |
7.622998e-07 |
| c5.GO_CELL_PART_MORPHOGENESIS |
556 |
16.49 |
38 |
2.30 |
1.544832e-06 |
| c5.GO_B_CELL_MEDIATED_IMMUNITY |
40 |
1.19 |
9 |
7.59 |
1.979220e-06 |
| c5.GO_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS |
867 |
25.71 |
51 |
1.98 |
2.241517e-06 |
| c2.CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 |
397 |
11.77 |
30 |
2.55 |
2.781861e-06 |

Effective sample size calculations

SessionInfo
## R version 3.3.2 (2016-10-31)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 14.04.5 LTS
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] grid stats4 compiler parallel stats graphics grDevices
## [8] datasets utils methods base
##
## other attached packages:
## [1] OIdata_1.0 maps_3.1.1
## [3] RCurl_1.95-4.8 bitops_1.0-6
## [5] sets_1.0-17 VennDiagram_1.6.17
## [7] futile.logger_1.4.3 ggbio_1.22.3
## [9] EnsDb.Hsapiens.v70_0.0 ensembldb_1.6.2
## [11] GenomicFeatures_1.26.2 WGCNA_1.51
## [13] fastcluster_1.1.22 dynamicTreeCut_1.63-1
## [15] lmerTest_2.0-33 lme4_1.1-12
## [17] Matrix_1.2-8 pheatmap_1.0.8
## [19] GSEABase_1.36.0 graph_1.52.0
## [21] annotate_1.52.1 XML_3.98-1.5
## [23] AnnotationDbi_1.36.2 HTSanalyzeR_2.26.0
## [25] igraph_1.0.1 gage_2.24.0
## [27] GGally_1.3.0 knitr_1.15.1
## [29] qvalue_2.6.0 reshape2_1.4.2
## [31] xtable_1.8-2 colortools_0.1.5
## [33] preprocessCore_1.36.0 DESeq2_1.14.1
## [35] SummarizedExperiment_1.4.0 GenomicRanges_1.26.2
## [37] GenomeInfoDb_1.10.3 IRanges_2.8.1
## [39] S4Vectors_0.12.1 readr_1.0.0
## [41] latex2exp_0.4.0 mixtools_1.0.4
## [43] ape_4.1 ggrepel_0.6.5
## [45] variancePartition_1.5.9 Biobase_2.34.0
## [47] BiocGenerics_0.20.0 ggplot2_2.2.1
## [49] gridExtra_2.2.1 edgeR_3.16.5
## [51] limma_3.28.21 synapseClient_1.14-2
## [53] doParallel_1.0.10 iterators_1.0.8
## [55] foreach_1.4.3
##
## loaded via a namespace (and not attached):
## [1] backports_1.0.5 AnnotationHub_2.6.4
## [3] Hmisc_4.0-2 plyr_1.8.4
## [5] lazyeval_0.2.0 splines_3.3.2
## [7] gmp_0.5-13 BiocParallel_1.8.1
## [9] digest_0.6.12 BiocInstaller_1.24.0
## [11] htmltools_0.3.5 GO.db_3.4.0
## [13] gdata_2.17.0 magrittr_1.5
## [15] checkmate_1.8.2 memoise_1.0.0
## [17] BSgenome_1.42.0 cluster_2.0.5
## [19] prada_1.50.0 Biostrings_2.42.1
## [21] matrixStats_0.51.0 colorspace_1.3-2
## [23] rrcov_1.4-3 genefilter_1.56.0
## [25] impute_1.48.0 VariantAnnotation_1.20.2
## [27] survival_2.40-1 gtable_0.2.0
## [29] zlibbioc_1.20.0 XVector_0.14.0
## [31] RankProd_3.0.0 cellHTS2_2.38.0
## [33] Rmpfr_0.6-1 DEoptimR_1.0-8
## [35] scales_0.4.1 futile.options_1.0.0
## [37] vsn_3.42.3 mvtnorm_1.0-5
## [39] DBI_0.5-1 Rcpp_0.12.10
## [41] htmlTable_1.9 foreign_0.8-67
## [43] OrganismDbi_1.16.0 Formula_1.2-1
## [45] htmlwidgets_0.8 httr_1.2.1
## [47] gplots_3.0.1 RColorBrewer_1.1-2
## [49] acepack_1.4.1 reshape_0.8.6
## [51] nnet_7.3-12 locfit_1.5-9.1
## [53] labeling_0.3 munsell_0.4.3
## [55] tools_3.3.2 RSQLite_1.1-2
## [57] evaluate_0.10 stringr_1.2.0
## [59] yaml_2.1.14 robustbase_0.92-7
## [61] caTools_1.17.1 KEGGREST_1.14.0
## [63] RBGL_1.50.0 nlme_3.1-131
## [65] mime_0.5 BioNet_1.34.0
## [67] biomaRt_2.30.0 pbkrtest_0.4-6
## [69] interactiveDisplayBase_1.12.0 png_0.1-7
## [71] affyio_1.44.0 statmod_1.4.29
## [73] tibble_1.2 geneplotter_1.52.0
## [75] pcaPP_1.9-61 stringi_1.1.2
## [77] highr_0.6 lattice_0.20-34
## [79] nloptr_1.0.4 data.table_1.10.4
## [81] httpuv_1.3.3 rtracklayer_1.34.2
## [83] colorRamps_2.3 R6_2.2.0
## [85] latticeExtra_0.6-28 affy_1.52.0
## [87] KernSmooth_2.23-15 codetools_0.2-15
## [89] lambda.r_1.1.9 dichromat_2.0-0
## [91] boot_1.3-18 MASS_7.3-45
## [93] gtools_3.5.0 assertthat_0.1
## [95] Category_2.40.0 rprojroot_1.2
## [97] rjson_0.2.15 GenomicAlignments_1.10.0
## [99] Rsamtools_1.26.1 rpart_4.1-10
## [101] minqa_1.2.4 rmarkdown_1.3
## [103] segmented_0.5-1.4 biovizBase_1.22.0
## [105] shiny_1.0.0 base64enc_0.1-3